SAXSdb — 4olf

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Proline--tRNA ligase

Plasmodium falciparum

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 249–746	Fragment：UNP residues 249-746	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 HFG 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one × 1 SO4 SULFATE ION × 15 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for 5min, then added 1 to 1 with Wiz3/4(h5)- 20%PEG-8000, 0.1M HEPES/NaOH, pH=7.5, 10% isopropanol, 0.2M AmSO4, cryoprotected with 20%EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.90 Å R-free 0.236
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 249–746	Fragment：UNP residues 249-746	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 HFG 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one × 2 SO4 SULFATE ION × 30 NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for 5min, then added 1 to 1 with Wiz3/4(h5)- 20%PEG-8000, 0.1M HEPES/NaOH, pH=7.5, 10% isopropanol, 0.2M AmSO4, cryoprotected with 20%EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.90 Å R-free 0.236

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4OLF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NCX Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum 3D7 Deposited 2013-10-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 249–746（498 aa） Fragment：C-terimus residues 249-746 Chain B 249–746（498 aa） Fragment：C-terimus residues 249-746	Not recorded	EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；Morpheus(b2): 0.1M each MES, Imidazole, pH 6.5, 0.09M each NaF, NaBr, NaI, 30% ethylene glycol, PEG-8000 and 5mM L-Proline, 5mM ATP, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 1.85 Å R-free 0.206
4Q15 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Halofuginone and AMPPNP in space group P212121 at 2.35 A Deposited 2014-04-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 249–746（498 aa） Fragment：UNP residues 249-746	Not recorded	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 HFG 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for ~5min, then added 1 to 1 with Wiz1/2(a10): 20% PEG-2000 MME, 0.1M Tris base/HCl, pH=7.0, cryoprotected with 20%EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.35 Å R-free 0.219
4Q15 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Halofuginone and AMPPNP in space group P212121 at 2.35 A Deposited 2014-04-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 249–746（498 aa） Fragment：UNP residues 249-746	Not recorded	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 HFG 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for ~5min, then added 1 to 1 with Wiz1/2(a10): 20% PEG-2000 MME, 0.1M Tris base/HCl, pH=7.0, cryoprotected with 20%EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.35 Å R-free 0.219
4Q15 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Halofuginone and AMPPNP in space group P212121 at 2.35 A Deposited 2014-04-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 249–746（498 aa） Fragment：UNP residues 249-746 Chain B 249–746（498 aa） Fragment：UNP residues 249-746	Not recorded	MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 HFG 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one × 2 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for ~5min, then added 1 to 1 with Wiz1/2(a10): 20% PEG-2000 MME, 0.1M Tris base/HCl, pH=7.0, cryoprotected with 20%EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.35 Å R-free 0.219
4TWA Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium falciparum Deposited 2014-06-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 254–746（493 aa） Fragment：UNP residues 254-746 Chain B 254–746（493 aa） Fragment：UNP residues 254-746	Not recorded	CL CHLORIDE ION × 6 SO4 SULFATE ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.8 M lithium sulphate monohydrate and 0.1 M sodium acetate	Resolution 3.00 Å R-free 0.249
4TWA Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium falciparum Deposited 2014-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 254–746（493 aa） Fragment：UNP residues 254-746 Chain B 254–746（493 aa） Fragment：UNP residues 254-746	Not recorded	CL CHLORIDE ION × 12 SO4 SULFATE ION × 22	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.8 M lithium sulphate monohydrate and 0.1 M sodium acetate	Resolution 3.00 Å R-free 0.249
4WI1 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with TCMDC-124506 Deposited 2014-09-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 249–746（498 aa） Fragment：UNP residues 249-746	Not recorded	3O6 1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]urea × 1 EDO 1,2-ETHANEDIOL × 7 MG MAGNESIUM ION × 1 IMD IMIDAZOLE × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；at 21.9mg/ml, incubated with 5mM TCMDC-124506, then 1:1 with Morpheus(B2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each magnesium chloride, calcium chloride	Resolution 1.65 Å R-free 0.188
4WI1 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with TCMDC-124506 Deposited 2014-09-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 249–746（498 aa） Fragment：UNP residues 249-746	Not recorded	3O6 1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]urea × 1 EDO 1,2-ETHANEDIOL × 7 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；at 21.9mg/ml, incubated with 5mM TCMDC-124506, then 1:1 with Morpheus(B2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each magnesium chloride, calcium chloride	Resolution 1.65 Å R-free 0.188
4WI1 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with TCMDC-124506 Deposited 2014-09-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 249–746（498 aa） Fragment：UNP residues 249-746 Chain B 249–746（498 aa） Fragment：UNP residues 249-746	Not recorded	3O6 1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]urea × 4 EDO 1,2-ETHANEDIOL × 28 MG MAGNESIUM ION × 2 IMD IMIDAZOLE × 4 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；at 21.9mg/ml, incubated with 5mM TCMDC-124506, then 1:1 with Morpheus(B2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each magnesium chloride, calcium chloride	Resolution 1.65 Å R-free 0.188
4YDQ Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium falciparum in complex with Halofuginone and AMPPNP Deposited 2015-02-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 254–746（493 aa） Fragment：UNP residues 254-746 Chain B 254–746（493 aa） Fragment：UNP residues 254-746	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 HFG 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Bis-Tris pH 6.5, 2 % (v/v) Tacsimate pH 5.0 and 12 % (w/v) Polyethylene glycol 3,350.	Resolution 2.30 Å R-free 0.232
5IFU Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Glyburide Deposited 2016-02-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 249–746（498 aa） Fragment：UNP residues 249-746	Not recorded	GBM 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide × 1 CL CHLORIDE ION × 1 FMT FORMIC ACID × 10 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；at 22mg/ml, incubated with 5mM glyburide, then 1:1 with Morpheus(g2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each sodium formate, ammonium acetate, trisodium citrate, sodium potassium tartrate, sodium oxamate	Resolution 2.45 Å R-free 0.213
5IFU Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Glyburide Deposited 2016-02-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 249–746（498 aa） Fragment：UNP residues 249-746	Not recorded	GBM 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide × 1 FMT FORMIC ACID × 4 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；at 22mg/ml, incubated with 5mM glyburide, then 1:1 with Morpheus(g2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each sodium formate, ammonium acetate, trisodium citrate, sodium potassium tartrate, sodium oxamate	Resolution 2.45 Å R-free 0.213
5IFU Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Glyburide Deposited 2016-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 249–746（498 aa） Fragment：UNP residues 249-746 Chain B 249–746（498 aa） Fragment：UNP residues 249-746	Not recorded	GBM 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide × 4 CL CHLORIDE ION × 2 FMT FORMIC ACID × 28 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；at 22mg/ml, incubated with 5mM glyburide, then 1:1 with Morpheus(g2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each sodium formate, ammonium acetate, trisodium citrate, sodium potassium tartrate, sodium oxamate	Resolution 2.45 Å R-free 0.213
6T7K Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with NCP-26 and L-Proline Deposited 2019-10-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 249–746（498 aa）	Not recorded	PRO PROLINE × 1 MU5 ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-(piperidin-1-ylcarbonylamino)pyrazine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 21	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1 M Hepes pH 7.5 20% PEG 1000, 2 mM Pro	Resolution 1.79 Å R-free 0.194
7F96 Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L95 Deposited 2021-07-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 254–746（493 aa） Fragment：UNP residues 254-746	Not recorded	JE6 ~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide × 2 PRO PROLINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.2 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Tris (base); BICINE) and 30 % v/v Precipitant Mix (40% v/v Ethylene glycol; 20% w/v PEG 8000)	Resolution 2.58 Å R-free 0.191
7F97 Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L97 Deposited 2021-07-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 254–746（493 aa） Fragment：UNP residues 254-746 Chain B 254–746（493 aa） Fragment：UNP residues 254-746	Not recorded	PRO PROLINE × 2 1XK 4-[(3S)-3-cyclopropyl-3-(hydroxymethyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide × 2 BU1 1,4-BUTANEDIOL × 1 CL CHLORIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Tris (base), BICINE), 37.5 % v/v Precipitant (25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350)	Resolution 2.39 Å R-free 0.232
7F97 Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L97 Deposited 2021-07-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 254–746（493 aa） Fragment：UNP residues 254-746 Chain D 254–746（493 aa） Fragment：UNP residues 254-746	Not recorded	PRO PROLINE × 2 1XK 4-[(3S)-3-cyclopropyl-3-(hydroxymethyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide × 2 CL CHLORIDE ION × 4 HEZ HEXANE-1,6-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Tris (base), BICINE), 37.5 % v/v Precipitant (25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350)	Resolution 2.39 Å R-free 0.232
7QB7 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT345 and L-Proline Deposited 2021-11-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 249–746（498 aa）	Not recorded	PRO PROLINE × 1 EDO 1,2-ETHANEDIOL × 13 9X2 ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-[[4-[[[(2~{S})-pyrrolidin-2-yl]carbonylamino]methyl]piperidin-1-yl]carbonylamino]pyrazine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；25% PEG3350, 0.1M Bis-Tris	Resolution 1.90 Å R-free 0.210
7QC1 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT436 Deposited 2021-11-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 249–746（498 aa）	Not recorded	9XM [(2~{R},3~{S})-2-[3-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanylidene-propyl]piperidin-3-yl] ~{N}-[4-[[3-(2,3-dihydro-1~{H}-inden-2-ylcarbamoyl)pyrazin-2-yl]carbamoyl]piperazin-1-yl]sulfonylcarbamate × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；1.5 M Malic acid	Resolution 2.51 Å R-free 0.233
7QC1 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT436 Deposited 2021-11-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 249–746（498 aa）	Not recorded	9XM [(2~{R},3~{S})-2-[3-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanylidene-propyl]piperidin-3-yl] ~{N}-[4-[[3-(2,3-dihydro-1~{H}-inden-2-ylcarbamoyl)pyrazin-2-yl]carbamoyl]piperazin-1-yl]sulfonylcarbamate × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；1.5 M Malic acid	Resolution 2.51 Å R-free 0.233
7QC1 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT436 Deposited 2021-11-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 249–746（498 aa）	Not recorded	9XM [(2~{R},3~{S})-2-[3-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanylidene-propyl]piperidin-3-yl] ~{N}-[4-[[3-(2,3-dihydro-1~{H}-inden-2-ylcarbamoyl)pyrazin-2-yl]carbamoyl]piperazin-1-yl]sulfonylcarbamate × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；1.5 M Malic acid	Resolution 2.51 Å R-free 0.233
7QC2 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT334 and L-Proline Deposited 2021-11-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 249–746（498 aa）	Not recorded	PRO PROLINE × 1 AJT ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-[[4-[[(2~{S})-pyrrolidin-2-yl]carbonylamino]piperidin-1-yl]carbonylamino]pyrazine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.2 M L-Pro, 10 % PEG3350, 0.1 M Hepes	Resolution 2.28 Å R-free 0.253
7V9D Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with inhibitor L95 and azetidine Deposited 2021-08-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 254–746（493 aa）	Not recorded	JE6 ~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide × 2 02A (2S)-azetidine-2-carboxylic acid × 2 EDO 1,2-ETHANEDIOL × 6 ACT ACETATE ION × 2 BU1 1,4-BUTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.12 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Imidazole, MES monohydrate), 30 % v/v Precipitant (40% v/v Ethylene glycol, 20% w/v PEG 8000)	Resolution 1.94 Å R-free 0.200
9YON Crystal structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with inhibitor YNW69 Deposited 2025-10-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 249–746（498 aa） Fragment：UNP residues 249-746	Not recorded	CL CHLORIDE ION × 10 SO4 SULFATE ION × 10 A1CYM N-[(3M)-3-(4-aminothieno[3,2-d]pyrimidin-6-yl)benzene-1-sulfonyl]-L-prolinamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；Grid Salt screen H8 : 4.0M NaCl, 0.1M Citric acid/citrate, pH 5.0. CrpaA.01302.a.B2.PW39348 at 21.9 mg/mL. 2mM inhibitor added to the protein prior to crystallization. plate 19968 H8 drop 1, Puck: PSL-1107, Cryo: 2.5M Lithium sulfate. The data were somewhat anisotropic which produced residual density (Fo-Fc) thoughout the polypeptide. The anisotropically truncated data from staraniso were used for refinement. The original and anisotropic truncated data were both deposited.	Resolution 2.43 Å R-free 0.233

14 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SYP_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–506； UniProt 249–746

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4olf
Deposition date deposition_date	2014-01-23
Structure title title	Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase)from Plasmodium falciparum in complex with Halofuginone and AMPPNP
Keywords keywords	;Structural Genomics, NIAID, National Institute of Allergy and Infectious Diseases, Seattle Structural Genomics Center for Infectious Disease, SSGCID, Prolyl-tRNA synthetase, ligase ;; LIGASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.10 Å
Radius of gyration Rg (electron density) rg_electron	25.31 Å
Forward intensity I(0) i0	55057000.00
Molecular weight molecular_weight	55885.0 kDa
Excluded volume excluded_volume	68840 Å³
Envelope volume envelope_volume	83023 Å³
Hydration-shell volume shell_volume	28020 Å³
Envelope diameter envelope_diameter	93.9 Å
Shell Rg shell_rg	32.04 Å
Envelope Rg envelope_rg	25.91 Å
Shape Rg shape_rg	25.33 Å
Total Rg total_rg	25.94 Å
Total atoms total_atoms	3908
Residues n_residues	482
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	88.7 Å
Rg (real space) rg_real	26.13 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	5.5060e+07
I(0) uncertainty (real space) i0_real_error	7.6900e+05
Rg (reciprocal space) rg_reciprocal	26.13 Å
I(0) (reciprocal space) i0_reciprocal	55060000.0000
Solution quality estimate total_estimate	0.8785
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.399
Kurtosis Kurtosis kurtosis	-0.297
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12880000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Proline--tRNA ligase
Molecular weight formula_weight	58986.5 kDa
EC 编号 ec_number	6.1.1.15
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3916

MAHHHHHHSNILGITSKKIENFSDWYTQVIVKSELIEYYDISGCYILRPAAYYIWECVQAFFNKEIKKLNVENSYFPLFVTKNKLEKEKNHIEGFSPEVAWVTKYGDSNLPEEIAIRPTSETIMYSVFPKWIRSYRDLPLKLNQWNTVVRWEFKQPTPFIRTREFLWQEGHTAHKNEEEAVKLVFDILDLYRRWYEEYLAVPIIKGIKSEGEKFGGANFTSTAEAFISENGRAIQAATSHYLGTNFAKMFKIEFEDENEVKQYVHQTSWGCTTRSIGIMIMTHGDDKGLVLPPNVSKYKVVIVPIFYKTTDENAIHSYCKDIEKILKNAQINCVYDDRASYSPGYKFNHWELRGIPIRIEVGPKDLQNNSCVIVRRDNNEKCNVKKESVLLETQQMLVDIHKNLFLKAKKKLDDSIVQVTSFSEVMNALNKKKMVLAPWCEDIATEEEIKKETQRLSLNQTNSETTLSGAMKPLCIPLDQPPMPPNMKCFWSGKPAKRWCLFGRSY

来源 Source

来源生物 organism	Plasmodium falciparum
NCBI Class编号 ncbi_taxonomy_id	36329
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one
Molecular weight formula_weight	414.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4olfA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	4olfA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	4olfA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	30 — C-terminal domain of ProRS

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8. Citations (1)

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Unit-cell length a length_a	106.550 Å
Unit-cell length b length_b	106.550 Å
Unit-cell length c length_c	186.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	46.237 Å
R factor r_factor	0.1994
R_work r_work	0.1976
R_free r_free	0.2363

fit	/app/data/saxs_computation/ol/4olf/4olf.fit
pddf	/app/data/pr_computation/ol/4olf/4olf.pr.out
profile	/app/data/saxs_computation/ol/4olf/4olf.dat

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase)from Plasmodium falciparum in complex with Halofuginone and AMPPNP